This project contains scripts used for working with Illumina sequencer run data, including HiSeq 2000/2500, MiSeqs and NextSeqs.
- Report : contains the wideInstrumentReport for reading Illumina interop files and BamQC JSON files and reporting on lane-by-lane statistics
- Check and Clean : contains scripts for cleaning run directories once data has been generated
This code has been produced by Genome Sequence Informatics for Ontario Institute for Cancer Research. Send any questions to gsi@oicr.on.ca .
The repository is 'private' because no one else has the same setup as OICR, and because digging through git history to see if any passwords were ever committed seems tiresome.
Nevertheless, the code is licensed under MIT and can be distributed freely.